I used to have that problem with Cyberduck until I disabled multiple connections. It's much better now. I do find that my 3DS seems to drop WiFi while I'm in homebrew unless I keep a constant ping going in the background, but I think that might have more to do with my Unifi routers than anything else.
I've never used FileZilla, but looking at the screenshot it looks like this is what you need to do. On the toolbar, put the IP address in the Host field. Enter anonymous as the username, and 5000 as the port. Then press Quick Connect. The right hand pane labelled Remote Site should then show the contents of your 3DS SD card. You can browse the two panes to get to the source/destination folders on the local and remote side and then drag and drop files between them.
I'm getting "connection refused by server" as an error message. Do I need to set up a server on my computer? Rather, if I switched programs, would you be able to help better? Cuz I'm not that picky.
No, the server is running on the 3DS. If the connection is refused then that means the IP address or port is wrong, or the server isn't running.
Depends what is running the firewall. If the firewall is running on your computer then you configure it on the computer. If it's on your router then you use the router's web interface.
If you download the ftbrony source and go into the /data/ folder there should be a banner.bin file. Open it in a hex editor, replace ALL data with 0's, and recompile. You now have a good FTP server with no ponies on the bottom screen.
